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@STRING{lncs = {Lecture Notes in Computer Science}}

@STRING{mibi = {Medizinische Informatik und Bioinformatik}}

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@ARTICLE{AchVayBar01,
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  author = {Hofmann, E.}
}

@BOOK{Hol85,
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}

@PROCEEDINGS{Hol94,
  title = {{The inherited metabolic diseases (2.Ed.)}},
  year = {1994},
  editor = {Holton, J. B.},
  publisher = {Edinburgh: Churchill Livingstone}
}

@ARTICLE{HooVriSan96,
  author = {Hooft, R. and Vriend, G. and Sander, C. and Abolda, E. E.},
  title = {{ Molecular Database Analysis}},
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@BOOK{HorCor00,
  title = {{ Core Java 2, Bd. 2 Expertenwissen}},
  publisher = {{Markt und Technik}},
  year = {2000},
  author = {Horsmann, C. S. and Cornell, G.}
}

@BOOK{HorCor99,
  title = {{ Core Java 2, Bd. 1 Grundlagen}},
  publisher = {{Markt und Technik}},
  year = {1999},
  author = {Horsmann, C. S. and Cornell, G.}
}

@UNPUBLISHED{hsql,
  author = {{HSQLDB Development Group}},
  title = {HSQLDB - Lightweight 100\% Java SQL Database Engine},
  note = {http://www.hsql.org},
  key = {hsql}
}

@TECHREPORT{Hu04,
  author = {Hu, Z.},
  title = {{Guidelines for Protein Name Tagging Version 2.0}},
  institution = {{Protein Information Resource, Georgetown University Medical Center
	and Department of Linguistics, Georgetown University}},
  year = {2004},
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}

@ARTICLE{HuaMad99,
  author = {Huang, X. and Madan, A.},
  title = {{ CAP3: A DNA Sequence Assembly Program}},
  journal = {{Genome Research}},
  year = {1999},
  volume = {9},
  pages = {{868--877}},
  number = {9}
}

@ARTICLE{HubBarBir02,
  author = {Hubbard, T. and Barker, D. and Birney, E. and Cameron, G. and Chen,
	Y. and Clark, L. and Cox, T. and Cuff, J. and Curwen, V. and Down,
	T. and Durbin, R. and Eyras, E. and Gilbert, J. and Hammond, M. and
	Huminiecki, L. and Kasprzyk, A. and Lehvaslaiho, H. and Lijnzaad,
	P. and Melsopp, C. and Mongin, E. and Pettett, P. and Pocock, M.
	and Potter, S. and Rust, R. and Schmidt, E. and Searle, S. and Slater,
	G. and Smith, J. and Spooner, W. and Stabenau, A. and Stalker, J.
	and Stupka, E. and Ureta-Vidal, A. and Vastrik, I. and Clamp, M.},
  title = {{ The Ensembl genome database project}},
  journal = {{Nucleic Acids Research}},
  year = {2002},
  volume = {30},
  pages = {{38--41}},
  number = {1}
}

@ARTICLE{HucFinSau03,
  author = {Hucka, M. and Finney, A. and Sauro, H. M. and Bolouri, H. and Doyle,
	J. C. and Kitano, H. and and the rest of the SBML Forum:, and Arkin,
	A. P. and Bornstein, B. J. and Bray, D. and Cornish-Bowden, A. and
	Cuellar, A. A. and Dronov, S. and Gilles, E. D. and Ginkel, M. and
	Gor, V. and Goryanin, I. I. and Hedley, W. J. and Hodgman, T. C.
	and Hofmeyr, J.-H. and Hunter, P. J. and Juty, N. S. and Kasberger,
	J. L. and Kremling, A. and Kummer, U. and Le Novere, N. and Loew,
	L. M. and Lucio, D. and Mendes, P. and Minch, E. and Mjolsness, E.
	D. and Nakayama, Y. and Nelson, M. R. and Nielsen, P. F. and Sakurada,
	T. and Schaff, J. C. and Shapiro, B. E. and Shimizu, T. S. and Spence,
	H. D. and Stelling, J. and Takahashi, K. and Tomita, M. and Wagner,
	J. and Wang, J.},
  title = {{The systems biology markup language (SBML): a medium for representation
	and exchange of biochemical network models}},
  journal = {Bioinformatics},
  year = {2003},
  volume = {19},
  pages = {524-531},
  number = {4},
  note = {{{http://www.sbw-sbml.org/sbml/docs/}}},
  abstract = {Motivation: Molecular biotechnology now makes it possible to build
	elaborate systems models, but the systems biology community needs
	information standards if models are to be shared, evaluated and developed
	cooperatively. Results: We summarize the Systems Biology Markup Language
	(SBML) Level 1, a free, open, XML-based format for representing biochemical
	reaction networks. SBML is a software-independent language for describing
	models common to research in many areas of computational biology,
	including cell signaling pathways, metabolic pathways, gene regulation,
	and others. Availability: The specification of SBML Level 1 is freely
	available from http://www.sbml.org/ Contact: sysbio-team@caltech.edu},
  doi = {10.1093/bioinformatics/btg015},
  eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/19/4/524.pdf},
  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/4/524}
}

@PROCEEDINGS{HucToe93,
  title = {{ K{\"u}nstliche Intelligenz in der Medizin: Klinisch- methologische
	Aspekte medizinischer Expertensysteme}},
  year = {1993},
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}

@ARTICLE{HueSalThi98,
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  journal = {{Nucleic Acids Research}},
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  volume = {26},
  pages = {{55--60}},
  number = {1}
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@ARTICLE{HuManHer04,
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  year = {2004},
  volume = {28},
  pages = {409 - 416},
  number = {5-6}
}

@BOOK{Hun98,
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  author = {Hunt, C.}
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@UNPUBLISHED{icd10,
  author = {{National Center for Health Statistics}},
  title = {{International Classification of Diseases, Tenth Revision, Clinical
	Modification (ICD-10-CM)}},
  note = {http://www.cdc.gov/nchs/about/otheract/icd9/icd10cm.htm},
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}

@article{IdeLoaDem07,
author = {Ide, Nicholas C. and Loane, Russell F. and Demner-Fushman, Dina},
title = {{Essie: A Concept-based Search Engine for Structured Biomedical Text}},
journal = {Journal of  the American Medical Informatics Association},
volume = {14},
number = {3},
pages = {253-263},
year = {2007}
}


@MANUAL{igddoc,
  title = {{IGD: The Integrated Genomic Database}},
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@ARTICLE{IkeIshGoj03,
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  volume = {326},
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  number = {10}
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@ARTICLE{IliTsoAnd03,
  author = {Iliopoulos, I. and Tsoka, S. and Andrade, M. A. and Enright, A. J.
	and Carroll, M. and Poullet, P. and Promponas, V. and Liakopoulos,
	T. and Palaios, G. and Pasquier, C. and Hamodrakas, S. and Tamames,
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	C. and Valencia, A. and Brett, D. and Martin, D. and Leroy, C. and
	Rigoutsos, I. and Sander, C. and Ouzounis, C. A.},
  title = {{Evaluation of annotation strategies using an entire genome sequence}},
  journal = {Bioinformatics},
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  volume = {19},
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  number = {6}
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@BOOK{Inm02,
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  year = {2002},
  author = {Inmon, W. H.},
  address = {New York, NY, USA}
}

@BOOK{Inm05,
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  publisher = {John Wiley \& Sons},
  year = {2005},
  author = {Inmon, W.H.},
  edition = {4th},
  month = {October},
  isbn = {0764599445},
  language = {english}
}

@ARTICLE{InmFloMay01,
  author = {Inman, J. T. and Flores, H. R. and May, G. D. and 
	
	 Weller, J. W. and Bell, C. J.},
  title = {{ A high-throughput distributed DNA sequence analysis
	
	 and database system}},
  journal = {{IBM Systems Journal}},
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  volume = {40},
  pages = {464--486},
  number = {2}
}

@MANUAL{ISO99,
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@ARTICLE{JaiAvrIli05,
  author = {Jaiswal, P. and Avraham, S. and Ilic, K. and Kellogg, E.A. and McCouch,
	S. and Pujar, A. and Reiser, L. and Rhee, S.Y. and Sachs, M.M. and
	Schaeffer, M. and others},
  title = {{Plant Ontology (PO): a controlled vocabulary of plant structures
	and growth stages}},
  journal = {Comparative and Functional Genomics},
  year = {2005},
  volume = {6},
  pages = {388--397},
  number = {7-8}
}

@ARTICLE{JaiNiYap06,
  author = {Jaiswal, P. and Ni, J. and Yap, I.l and Ware, D. and Spooner, W.
	and Youens-Clark, K. and Ren, L. and Liang, C. and Zhao, W. and Ratnapu,
	K. and Faga, B. and Canaran, P. and Fogleman, M. and Hebbard, C.
	and Avraham, S. and Schmidt, S. and Casstevens, T.M. and Buckler,
	E.S. and Stein, L. and McCouch, S.},
  title = {{Gramene: a bird's eye view of cereal genomes}},
  journal = {Nucl. Acids Res.},
  year = {2006},
  volume = {34},
  pages = {D717-723},
  number = {suppl_1},
  abstract = {Rice, maize, sorghum, wheat, barley and the other major crop grasses
	from the family Poaceae (Gramineae) are mankind's most important
	source of calories and contribute tens of billions of dollars annually
	to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov).
	Continued improvement of Poaceae crops is necessary in order to continue
	to feed an ever-growing world population. However, of the major crop
	grasses, only rice (Oryza sativa), with a compact genome of [~]400
	Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org)
	takes advantage of the known genetic colinearity (synteny) between
	rice and the major crop plant genomes to provide maize, sorghum,
	millet, wheat, oat and barley researchers with the benefits of an
	annotated genome years before their own species are sequenced. Gramene
	is a one stop portal for finding curated literature, genetic and
	genomic datasets related to maps, markers, genes, genomes and quantitative
	trait loci. The addition of several new tools to Gramene has greatly
	facilitated the potential for comparative analysis among the grasses
	and contributes to our understanding of the anatomy, development,
	environmental responses and the factors influencing agronomic performance
	of cereal crops. Since the last publication on Gramene database by
	D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L.
	Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant
	Physiol., 130, 1606-1613], the database has undergone extensive changes
	that are described in this publication.},
  doi = {10.1093/nar/gkj154},
  eprint = {http://nar.oxfordjournals.org/cgi/reprint/34/suppl_1/D717.pdf},
  owner = {scholz},
  url = {http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D717}
}

@TECHREPORT{Jak97,
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@INPROCEEDINGS{Jam00a,
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	Engineering, Washington, D.C., U.S.A., November 8-10}},
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  pages = {118-125},
  publisher = {{IEEE Computer Society}}
}

@UNPUBLISHED{javacc,
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  note = {https://javacc.dev.java.net},
  key = {javacc}
}

@article{JenSarBor06,
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	Pages = {119-129},
	Title = {{Literature mining for the biologist: from information retrieval to biological discovery}},
	Volume = {7},
	Year = {2006}}

@INCOLLECTION{JeuPap99,
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  editor = {Kraemer, Bernd and Papazoglou, Michael P. and Schmidt, Heinz-W.},
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@TECHREPORT{Joh78,
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@BOOK{Jos94,
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@ARTICLE{JunKluSch06,
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}

@INPROCEEDINGS{JusBarLeg03,
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@ARTICLE{KahWes91,
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@MASTERSTHESIS{Kam94,
  author = {Kampp, R.},
  title = {{ SEZUAN~--~Eine Simulations- und Entwicklungsumgebung f{\"u}r Zellulare
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@ARTICLE{Kan96,
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@ARTICLE{KanAldAlt05,
  author = {Kanz, C. and Aldebert, P. and Althorpe, N. and Baker, W. and Baldwin,
	A. and Bates, K. and Browne, P. and van den Broek, A. and Castro,
	M. and Cochrane, G. and Duggan, K. and Eberhardt, R. and Faruque,
	N. and Gamble, J. and Diez, F. G. and Harte, N. and Kulikova, T.
	and Lin, Q. and Lombard, V. and Lopez, R. and Mancuso, R. and McHale,
	M. and Nardone, F. and Silventoinen, V. and Sobhany, S. and Stoehr,
	P. and Tuli, M. A. and Tzouvara, K. and Vaughan, R. and Wu, D. and
	Zhu, W. and Apweiler, R.},
  title = {{ The EMBL Nucleotide Sequence Database}},
  journal = {Nucleic Acids Research},
  year = {2005},
  volume = {33},
  pages = {D29-33},
  number = {suppl\_1}
}

@ARTICLE{KanGot00,
  author = {Kanehisa, M. and Goto, S.},
  title = {{ KEGG: Kyoto Encyclopedia of Genes and Genomes}},
  journal = {{Nucleic Acids Research}},
  year = {2000},
  volume = {28},
  pages = {{27--30}},
  number = {1},
  note = {{http://www.genome.ad.jp/kegg/}}
}

@INPROCEEDINGS{KanGot97,
  author = {Kanehisa, M. and Goto, S. },
  title = {{ A Systematic Analysis of Gene Functions by the Metabolic Pathway
	database}},
  booktitle = {{ Theoretical and Computational Methods in Genome Research}},
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  editor = { Suhai, S.},
  pages = {41--56},
  publisher = {New York: Plenum Press}
}

@ARTICLE{KanGotKaw02,
  author = {Kanehisa, M. and Goto, S. and Kawashima, S. and Nakaya, A.},
  title = {{ The KEGG database at GenomeNet}},
  journal = {{Nucleic Acids Research}},
  year = {2002},
  volume = {30},
  pages = {{42--46}},
  number = {1},
  note = {{http://www.genome.ad.jp/kegg/}}
}

@ARTICLE{KanRotMat02,
  author = {Kantety, R. V. and {La Rota} M. and Matthews, D. E. and 
	
	 Sorrells, M. E.},
  title = {{ Data mining for simple sequence repeats in expressed 
	
	 sequence tags from barley, maize, rice, sorghum and wheat}},
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  year = {2002},
  volume = {48},
  pages = {501--510},
  number = {{5-6}}
}

@ARTICLE{KapHeuMai96,
  author = {Kaps, A. and Heumann, K. and Maierl, A. and Mewes, H.-W.},
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  year = {1996},
  volume = {38},
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@ARTICLE{KapKemCul04,
  author = {Kapushesky, Misha and Kemmeren, Patrick and Culhane, Aedin C. and
	Durinck, Steffen and Ihmels, Jan and Korner, Christine and Kull,
	Meelis and Torrente, Aurora and Sarkans, Ugis and Vilo, Jaak and
	Brazma, Alvis},
  title = {{Expression Profiler: next generation--an online platform for analysis
	of microarray data}},
  journal = {Nucl. Acids Res.},
  year = {2004},
  volume = {32},
  pages = {W465-470},
  number = {suppl_2},
  doi = {10.1093/nar/gkh470},
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  url = {http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_2/W465}
}

@ARTICLE{Kar00,
  author = {Karp, P. D.},
  title = {{ An ontology for biological function based on molecular interactions}},
  journal = {{Bioinformatics}},
  year = {2000},
  volume = {16},
  pages = {269--285},
  number = {3}
}

@ARTICLE{Kar92,
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  title = {{ A knowledge base of chemical compounds of intermediary metabolism}},
  journal = {{CABIOS}},
  year = {1992},
  volume = {8},
  pages = {347--357},
  number = {4},
  publisher = {Oxford: Oxford University Press}
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@ARTICLE{Kar95a,
  author = {Karp, P. D.},
  title = {{A Strategy for Database Interoperation}},
  journal = {{Journal of Computational Biology}},
  year = {1995},
  volume = {2},
  pages = {573--586},
  number = {4},
  publisher = {Berkeley: Mary Ann Liebert, Inc.}
}

@ARTICLE{KarAlt90,
  author = {Karlin, S. and Altschul, S. F.},
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@ARTICLE{KarMav94,
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  title = {{ Representing, analyzing, and synthesizing biochemical pathways}},
  journal = {{IEEE Expert}},
  year = {1994},
  volume = {9},
  pages = {11--21},
  optnumber = {000}
}

@INPROCEEDINGS{KarPal94,
  author = {Karp, P. D. and Paley, S.},
  title = {{ Automated Drawing of Metabolic Pathways}},
  booktitle = {{ Proceeding of the Third International Conference on Bioinformatics
	{\&} Genome Research}},
  year = {1994},
  editor = {Lim, H. A. and Cantor, C. R.},
  pages = {225--238},
  publisher = {Singapore et al.: World Scientific}
}

@TECHREPORT{KarPal95,
  author = {Karp, P. D. and Paley, S.},
  title = {{Integrated Access to Metabolic and Genomic Data}},
  institution = {Artifical Intelligenze Center SRI International},
  year = {1995},
  optnumber = {0},
  opttype = {0}
}

@ARTICLE{KarPal96,
  author = {Karp, P. and Paley, S.},
  title = {{ Integrated Access to Metabolic and Genomic Data}},
  journal = {{Journal of Computational Biology}},
  year = {1996},
  volume = {3},
  number = {1},
  optpages = {191--212}
}

@ARTICLE{KarPalZhu01,
  author = {Karp, P. and Paley, S. and Zhu, J.},
  title = {{ Database verification studies of SWISS--PROT and GenBank}},
  journal = {{Bioinformatics}},
  year = {2001},
  volume = {17},
  pages = {526--532},
  number = {6}
}

@INPROCEEDINGS{KarRil93,
  author = {Karp, P. D. and Riley, M.},
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  booktitle = {{ ISMB-93 Procceedings: First International Conference on Intelligent
	Systems for Molecular Biology}},
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@ARTICLE{KarRilSai00,
  author = {Karp, P. D. and Riley, M. and Saier, M. and Paulsen, I. T. and Paley,
	S. M. and Pellegrini-Toole, A.},
  title = {{ The EcoCyc and MetaCyc database}},
  journal = {{Nucleic Acids Research}},
  year = {2000},
  volume = {28},
  pages = {56--59},
  number = {1}
}

@ARTICLE{KasKeeSme04,
  author = {Kasprzyk, A. and Keefe, D. and Smedley, D. and London, D. and Spooner,
	W. and Melsopp, C. and Hammond, M. and Rocca-Serra, P. and Cox, T.
	and Birney, E.},
  title = {{EnsMart: A Generic System for Fast and Flexible Access to Biological
	Data}},
  journal = {Genome Research},
  year = {2004},
  volume = {14},
  pages = {160-169},
  number = {1}
}

@BOOK{KasShe00,
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}

@INPROCEEDINGS{RieDit95a,
  author = {B. Rieche and K. R. Dittrich},
  title = {{Einsatz und Nutzen einer Metaebene f{\"u}r f{\"o}derierte Datenbanksysteme
	am Beispiel der Molekularbiologie}},
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	Wissenschaft'' (BTW'95), Dresden, M{\"a}rz 1995}},
  year = {1995},
  editor = {G. Lausen},
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  address = {Berlin},
  publisher = {Springer-Verlag},
  annote = {checked}
}

@ARTICLE{RiiBobSal01,
  author = {Riikonen, P. and Boberg, J. and Salakoski, T. and Vihinen, M.},
  title = {{ BioWAP, mobile Internet service for bioinformatics}},
  journal = {{Bioinformatics}},
  year = {2001},
  volume = {17},
  pages = {{855--856}},
  number = {9}
}

@INPROCEEDINGS{Rit97,
  author = {Ritter, O.},
  title = {{ Comprehensive Genome Information Systems}},
  booktitle = {{ Theoretical and Computational Methods in Genome Research}},
  year = {1997},
  editor = { Suhai, S.},
  pages = {177--184},
  publisher = {New York et al.: Plenum Press}
}

@ARTICLE{RitKocSen94,
  author = {Ritter, O. and Kocab, P. and Senger, M. and Wolf, D. and Suhai, S.},
  title = {{ Prototype Implementation of the Integrated Genomic Database}},
  journal = {{Computers and Biomedical Research}},
  year = {1994},
  volume = {27},
  pages = {97--115},
  publisher = {San Diego: Academic Press, Inc.}
}

@ARTICLE{RitSuh96,
  author = {Ritter, O. and Suhai, S.},
  title = {{ Gigabytes {\"u}ber Gigabasen -- Informationsintegration in der
	Genomforschung}},
  journal = {{it+ti}},
  year = {1996},
  volume = {38},
  pages = {{16--19}},
  number = {5},
  publisher = {{M{\"u}nchen: Oldenbourg}}
}

@ARTICLE{RobBelBes03,
  author = {Roberts, R. J. and Belfort, M. and Bestor, T. and Bhagwat, A. S.
	and Bickle, T.A. and Bitinaite, J. and Blumenthal, R. M. and Degtyarev,
	S. K. and Dryden, D. T. F. and Dybvig, K. and Firman, K. and Gromova,
	E. S. and Gumport, R. I. and Halford, S. E. and Hattman, S. and Heitman,
	J. and Hornby, D. P. and Janulaitis, A. and Jeltsch, A. and Josephsen,
	J. and Kiss, A. and Klaenhammer, T. R. and Kobayashi, I. and Kong,
	H. and Kruger, D. H. and Lacks, S. and Marinus, M. G. and Miyahara,
	M. and Morgan, R. D. and Murray, N. E. and Nagaraja, V. and Piekarowicz,
	A. and Pingoud, A. and Raleigh, E. and Rao, D. N. and Reich, N. and
	Repin, V. E. and Selker, E. U. and Shaw, P.-C. and Stein, D. C. and
	Stoddard, B. L. and Szybalski, W. and Trautner, T. A. and Van Etten,
	J. L. and Vitor, J. M. B. and Wilson, G. G. and Xu, S.-Y.},
  title = {{ A nomenclature for restriction enzymes, DNA methyltransferases,
	homing endonucleases and their genes }},
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  number = {7}
}

@BOOK{Roc00,
  title = {{ XML, XLST, Java und JSP}},
  publisher = {{Galileo Press}},
  year = {2000},
  author = {Rockwell, W.}
}

@ARTICLE{RomFloLes03,
  author = {Rombauts, S. and Florquin, K. and Lescot, M. and Marchal, K. 
	
	 and Rouze, P. and {Van de Peer}, Y.},
  title = {{ Computational Approaches to Identify Promoters and 
	
	 cis-Regulatory Elements in Plant Genomes}},
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  year = {2003},
  volume = {132},
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  number = {3}
}

@ARTICLE{RonSteAsc03,
  author = {Ronning, C. M. and Stegalkina, S. S. and Ascenzi, R. A. and 
	
	 Bougri, O. and Hart, A. L. and Utterbach, T. R.
	
	
	 and Vanaken, S. E. and Riedmuller, S. B. and White, J. A. and 
	
	 Cho, J. and Pertea, G.M. and Lee, Y. and Karamycheva, S. and 
	
	 Sultana, R. and Tsai, J. and Quackenbush, J. and Griffiths, H. M.
	
	
	 and Restrepo, S. and Smart, C. D. and Fry, W. E. and 
	
	 {van der Hoeven}, R. and Tanksley, S. and Zhang, P. and Jin, H.
	
	 and Yamamoto, M. L. and Baker, B. J. and Buell, C. R.},
  title = {{ Comparative Analyses of Potato Expressed Sequence Tag Libraries}},
  journal = {{Plant Physiology}},
  year = {2003},
  volume = {131},
  pages = {{419--429}},
  number = {2}
}

@ARTICLE{Roo01,
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  title = {{ COMPUTATIONAL BIOLOGY: Bioinformatics--Trying to Swim in a Sea
	of Data}},
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  pages = {{1260--1261}},
  number = {5507}
}

@ARTICLE{RouDanHen93,
  author = {Rouxel, T. and Danchin, A. and Henaut, A.},
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	a graphics-oriented database}},
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  number = {3},
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}

@ARTICLE{Rud00,
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  title = {{ EcoGene: a genome sequence database for Escherichia coli K-12}},
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  year = {2000},
  volume = {28},
  pages = {{60--64}},
  number = {1}
}

@ARTICLE{RudMewMay03,
  author = {Rudd, S. and Mewes, H.-W. and Mayer, K. F. X.},
  title = {{ Sputnik: a database platform for comparative plant genomics}},
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  volume = {31},
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  number = {1}
}

@BOOK{SaaSat00,
  title = {{ Datenbanken und Java. JDBC, SQLJ und ODMG}},
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  year = {2000},
  author = {Saake, G. and Sattler, K.-U.}
}

@ARTICLE{SaaTroVal02,
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	 and Gruvberger, S. and Borg, A. and Peterson, C.},
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	 management and analysis of microarray data}},
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  year = {2002},
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  number = {8},
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}

@ARTICLE{SalCasGar91,
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@ARTICLE{SalSanGam00,
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	D. and Blattner, F. R. and Collado-Vides, J.},
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	organization in Escherichia coli K-12}},
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  number = {1}
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@ARTICLE{SalSanGam91,
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	D. and Diaz-Peredo, E. and Sanchez-Solano, F. and Perez-Rueda, E.
	and Bonavides-Martinez, C. and Collado-Vides, J.},
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	organization in Escherichia coli K-12}},
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  number = {1}
}

@ARTICLE{SalWooMav97,
  author = {Salenieks, A. and Woo, O. and Mavrovouniotis, M. L.},
  title = {{ Positive linear decomposition for classifying patterns in dynamic
	measurements: a case study}},
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  year = {1997},
  volume = {3},
  pages = {{155--167}},
  optnumber = {000}
}

@ARTICLE{SanSchPal03,
  author = {Sanchez-Villeda, H. and Schroeder, S. and Polacco, M. and McMullen,
	M. and Havermann, S. and Davis, G. and Vroh-Bi, I. and Cone, K. and
	Sharopova, N. and Yim, Y. and Schultz, L. and Duru, N. and Musket,
	T. and Houchins, K. and Fang, Z. and Gardiner, J. and Coe, E.},
  title = {{Development of an integrated laboratory information management system
	for the maize mapping project}},
  journal = {Bioinformatics},
  year = {2003},
  volume = {19},
  pages = {2022-2030},
  number = {16},
  abstract = {Motivation: The development of an integrated genetic and physical
	map for the maize genome involves the generation of an enormous amount
	of data. Managing this data requires a system to aid in genotype
	scoring for different types of markers coming from both local and
	remote users. In addition, researchers need an efficient way to interact
	with genetic mapping software and with data files from automated
	DNA sequencing. They also need ways to manage primer data for mapping
	and sequencing and provide views of the integrated physical and genetic
	map and views of genetic map comparisons. Results: The MMP-LIMS system
	has been used successfully in a high-throughput mapping environment.
	The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers
	have been entered and verified via MMP-LIMS. The system is flexible,
	and can be easily modified to manage data for other species. The
	software is freely available. Availability: To receive a copy of
	the iMap or cMap software, please fill out the form on our website.
	The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.},
  doi = {10.1093/bioinformatics/btg274},
  eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/19/16/2022.pdf},
  owner = {scholz},
  timestamp = {2006.12.08},
  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/16/2022}
}

@INPROCEEDINGS{SarFuhCri96,
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	and Mecklenburg, R. and Lindstrom, G. and Cartwright, P.},
  title = {{ The Design and Implementation of a Database For Human Genome Research}},
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	Systems, June 18--20, 1996, Stockholm, Sweden}},
  year = {1996},
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@ARTICLE{SarParLar05,
  author = {Sarkans, Ugis and Parkinson, Helen and Lara, Gonzalo Garcia and Oezcimen,
	Ahmet and Sharma, Anjan and Abeygunawardena, Niran and Contrino,
	Sergio and Holloway, Ele and Rocca-Serra, Philippe and Mukherjee,
	Gaurab and Shojatalab, Mohammadreza and Kapushesky, Misha and Sansone,
	Susanna-Assunta and Farne, Anna and Rayner, Tim and Brazma, Alvis},
  title = {{The ArrayExpress gene expression database: a software engineering
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  year = {2005},
  volume = {21},
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  number = {8},
  doi = {10.1093/bioinformatics/bti157},
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  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/8/1495}
}

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@ARTICLE{ScaMisBat05,
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  title = {{Data Quality at a Glance}},
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  year = {2005},
  volume = {14},
  pages = {6--14},
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}

@ARTICLE{Sch02,
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  pages = {179--193},
  number = {3},
  issn = {1386-6338},
  keywords = {owg},
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}

@ARTICLE{Sch97a,
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  title = {{Information Retrieval in Digital Libraries: Bringing Search to the
	Net}},
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  volume = {275},
  pages = {327--334},
  publisher = {Washington D.C.: AAAS}
}

@INPROCEEDINGS{Sch97b,
  author = {{Schulze-Kremer}, S.},
  title = {{ Adding Semantics to Genome Databases: Towards an Ontology for Molecular
	Biology}},
  booktitle = {{ Proceedings of the Fifth International Conference on Intelligent
	Systems for Molecular Biology }},
  year = {1997},
  pages = {272--275},
  publisher = {Greece. AAAI Press},
  opteditor = { XXX }
}

@INPROCEEDINGS{Sch98,
  author = {{Schulze-Kremer}, S.},
  title = {{ Ontologies for Molecular Biology}},
  booktitle = {{ Proceedings of the Third Pacific Symposium on Biocomputing}},
  year = {1998},
  editor = { XXX },
  pages = {693--704},
  publisher = {World Scientific Publishers, Singapor}
}

@INPROCEEDINGS{Sch98brenda,
  author = {Schomburg, D.},
  title = {{ BRENDA, Enzyme Data for Metabolic Simulations}},
  booktitle = {{Proceedings of the German Conference on Bioinformatics (GCB '98),
	K{\"o}ln, October 7-10}},
  year = {1998},
  editor = {Zimmermann, O. and Schomburg, D.},
  pages = {96--97},
  note = {{http://www.brenda.uni-koeln.de}},
  optpublisher = {XXX}
}

@ARTICLE{SchAeb85,
  author = {Schorderet, D. and Aebischer, P.},
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@BOOK{SchBanMer99,
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}

@BOOK{SchCar01,
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  year = {2001},
  author = {Schmid, E. and Cartus, C.}
}

@ARTICLE{SchChaSch02,
  author = {Schomburg, I. and Chang, A. and Schomburg, D.},
  title = {{ BRENDA, enzyme data and metabolic information}},
  journal = {{Nucleic Acids Research}},
  year = {2002},
  volume = {30},
  pages = {{47--49}},
  number = {1}
}

@ARTICLE{SchDavHen05,
  author = {Schmid, M. and Davison, T.S. and Henz, S.R. and Pape, U.J. and Demar,
	M. and Vingron, M. and Sch{\"o}lkopf, B. and Weigel, D. and Lohmann,
	J.U.},
  title = {{A gene expression map of Arabidopsis thaliana development}},
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}

@ARTICLE{SchEptOhk96,
  author = {Schuler, G.D. and Epstein, J.A. and Ohkawa, H. and Kans, J.A.},
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  volume = {266},
  pages = {{141--161}},
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}

@INPROCEEDINGS{SchSchCha99,
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  title = {{ BRENDA the Information System for Enzymes and metabolic Information}},
  booktitle = {{Proceedings of the German Conference on Bioinformatics (GCB '99),
	Hannover, October 4-6}},
  year = {1999},
  editor = {Giegerich, R. and Hofest{\"a}dt, R. and Lengauer, T. and Mewes, W.
	and Schomburg, D. and Vingron, M. and Wingender, E.},
  pages = {{226--227}},
  isbn = {{3-00-005121-X}},
  optpublisher = {{XXX}}
}

@ARTICLE{SchSchGra03,
  author = {Schwacke, R. and Schneider, A. and {van der Graaff}, E. and 
	
	 Fischer, K. and Catoni, E. and Desimone, M. and Frommer, W. B. 
	
	 and Flugge, U.-I. and Kunze, R.},
  title = {{ ARAMEMNON, a Novel Database for Arabidopsis Integral 
	
	 Membrane Proteins}},
  journal = {{Plant Physiology}},
  year = {2003},
  volume = {131},
  pages = {16--26},
  number = {1}
}

@PROCEEDINGS{SchSte98,
  title = {{ Enzyme Handbook}},
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  editor = {Schomburg, D. and Stephan, D.},
  volume = {15},
  publisher = {Heidelberg et. al: Springer}
}

@INPROCEEDINGS{SchWin99,
  author = {Schacherer, F. and Wingender, E.},
  title = {{ The Transpath Signal Transduction Database}},
  booktitle = {{Proceedings of the German Conference on Bioinformatics (GCB '99),
	Hannover, October 4--6}},
  year = {1999},
  editor = {Giegerich, R. and Hofest{\"a}dt, R. and Lengauer, T. and Mewes, W.
	and Schomburg, D. and Vingron, M. and Wingender, E.},
  pages = {{223--225}},
  isbn = {{3-00-005121-X}},
  optpublisher = {XXX}
}

@BOOK{ScoMer97,
  title = {{ Concise Encyclopedia Biochemistry and Molecular Biology, 3. Ed.}},
  publisher = {{Walter de Gruyte}},
  year = {1997},
  author = {Scott, T. A. and Mercer, E. I.}
}

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  title = {{ The metabolic and molecular bases of inherited disease (7.Ed.)}},
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  editor = {Scriver, C. R. and Beaudet, A. L. and Sly, W. S. and Valle, D.},
  publisher = {{New York: McGraw--Hill}}
}

@ARTICLE{Sea00,
  author = {Searls, D. B.},
  title = {{ Using bioinformatics in gene and drug discovery}},
  journal = {{Drug Discovery Today}},
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  volume = {5},
  pages = {135--143},
  number = {4}
}

@INBOOK{Sea93,
  chapter = {The Computational Linguistics of Biological Sequences},
  pages = {{47--119}},
  title = {Artifical Intelligence~{\&}~Molecular Biology},
  publisher = {Menlo Park et al.: AAAI Press~/~The MIT Press},
  year = {1993},
  author = {Searls, D. B.}
}

@ARTICLE{SelBasGaa96,
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	and Gretchkin, Y. and Maltsev, N. and Nenashev, V. and Overbeek,
	R. and Panyushkina, L. and {Selkov, Jr.}, E. and Yunus, I.},
  title = {{ The metabolic pathway collection from EMP: the enzymes and metabolic
	pathways database}},
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  year = {1996},
  volume = {24},
  pages = {26--28},
  number = {1},
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}

@ARTICLE{SelGreMik98,
  author = {Selkov, E. J. and Grechkin, Y. and Mikhailova, N. and Selkov, E.},
  title = {{ MPW: the Metabolic Pathways Database}},
  journal = {{Nucleic Acids Research}},
  year = {1998},
  volume = {26},
  pages = {43--45},
  number = {1}
}

@INPROCEEDINGS{SelMit97,
  author = {Sellentin, J. and Mitschang, B.},
  title = {{ M{\"o}glichkeiten und Grenzen des Einsatzes von CORBA in DB-basierten
	Client/Server-Anwendungssystemen (Kurzbeitrag)}},
  booktitle = {{ Datenbanken in B{\"u}ro, Technik und Wissenschaft - BTW'97, Ulm}},
  year = {1997},
  editor = {Dittrich, K. R. and Geppert, A.},
  pages = {312--321},
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}

@UNPUBLISHED{semanticweb,
  author = {{World Wide Web Consortium (W3C)}},
  title = {{Semantic Web}},
  note = {http://www.w3.org/2001/sw/},
  key = {semanticweb}
}

@ARTICLE{SenFloGla98,
  author = {Senger, M. and Flores, T. and Glatting, K.-H. and Ernst, P. and Hotz-Wagenblatt,
	A. and Suhai, S.},
  title = {{ W2H: WWW interface to the GCG sequence analysis package}},
  journal = {{Bioinformatics}},
  year = {1998},
  volume = {14},
  pages = {452--457},
  number = {5}
}

@ARTICLE{SenGlaRit95,
  author = {Senger, M. and Glatting, K.-H. and Ritter, O. and Suhai, S.},
  title = {{ X-Husar, an X-based graphical interface for the analysis of genomic
	sequences}},
  journal = {{Computer Methods and Programs in Biomedicine}},
  year = {1995},
  volume = {46},
  pages = {131--142},
  number = {2}
}

@INPROCEEDINGS{SenRicOin03,
  author = {Senger, M. and Rice, P. and Oinn, T.},
  title = {{SoapLab-a unified Sesame door to analysis tools.}},
  booktitle = {Proceedings of the UK e-Science All Hands Meeting 2003},
  year = {2003},
  publisher = {Nottingham, UK}
}

@BOOK{SetMei97,
  title = {{ Introduction to Computational Molecular Biology}},
  publisher = {Boston: PWS Publishing Company},
  year = {1997},
  author = {Setubal, J. and Meidanis, J.}
}

@ARTICLE{Sha03,
  author = {Shasha, D. E.},
  title = {{ Plant Systems Biology: Lessons from a Fruitful Collaboration}},
  journal = {{Plant Physiology}},
  year = {2003},
  volume = {132},
  pages = {{415--416}},
  number = {2}
}

@ARTICLE{ShaHuaXu05,
  author = {Shah, S. and Huang, Y. and Xu, T. and Yuen, M. and Ling, J. and Ouellette,
	B. F. F.},
  title = {Atlas - a data warehouse for integrative bioinformatics},
  journal = {BMC Bioinformatics},
  year = {2005},
  volume = {6},
  pages = {34},
  number = {1}
}

@ARTICLE{SheGonCal05,
  author = {Shen, L. and Gong, J. and Caldo, R. A. and Nettleton, D.n and Cook,
	D. and Wise, R. P. and Dickerson, J. A.},
  title = {{BarleyBase--an expression profiling database for plant genomics}},
  journal = {Nucl. Acids Res.},
  year = {2005},
  volume = {33},
  pages = {D614-618},
  number = {1},
  abstract = {BarleyBase (BB) (www.barleybase.org) is an online database for plant
	microarrays with integrated tools for data visualization and statistical
	analysis. BB houses raw and normalized expression data from the two
	publicly available Affymetrix genome arrays, Barley1 and Arabidopsis
	ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean
	and rice arrays, as they become available. BB contains a broad set
	of query and display options at all data levels, ranging from experiments
	to individual hybridizations to probe sets down to individual probes.
	Users can perform cross-experiment queries on probe sets based on
	observed expression profiles and/or based on known biological information.
	Probe set queries are integrated with visualization and analysis
	tools such as the R statistical toolbox, data filters and a large
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@url{IPK_databases,
Date-Added = {2011-07-25 02:19:13 +0200},
Date-Modified = {2011-07-25 02:19:13 +0200},
Title = {http://www.ipk-gatersleben.de/Internet/Infrastruktur/Datenbanken}}

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  pages = {537--546},
  number = {{2A}}
}

@BOOK{vHe90,
  title = {{Practical SGML}},
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  address = {Dordrecht, Netherlands},
  annote = {checked}
}

@BOOK{Vol31,
  title = {{ Lecon sur la Theorie Mathematique de la Lutte pour la Vie}},
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  author = {Volterra, V.}
}

@INPROCEEDINGS{Vos00,
  author = {Voss, K.},
  title = {{ Ausf{\"u}hrbare Petri Netz Modelle zur Simulation Metabolischer
	Pfade}},
  booktitle = {{Modellierung und Simulation Metabolischer Netzwerke: DFG-Workshop
	im Rahmen des DFG-Schwerpunktes Informatikmethoden zur Analyse und
	Interpretation gro{\ss{}}er genomischer Datenmengen, Magdeburg, 19.
	- 20. Mai 2000}},
  year = {2000},
  editor = {Hofest{\"a}dt, R. and Lautenbach, K. and Lange, M.},
  pages = {{11--13}},
  publisher = {{Fakult{\"a}t f{\"u}r Informatik, Universit{\"a}t Magdeburg}},
  optseries = {{Preprint Nr. xyz}}
}

@BOOK{Vos94,
  title = {{ Datenmodelle, Datenbanksprachen und Datenbank-Management-Systeme}},
  publisher = {{Bonn et al.: Addison-Wesley}},
  year = {1994},
  author = {Vossen, G.}
}

@MISC{W3CWS92,
  author = {{World Wide Web Consortium} {WS-W3C}},
  title = {Web Services},
  year = {2002},
  url = {www.w3.org/2002/ws/}
}

@ARTICLE{WaiLusDuc02,
  author = {H. M. Wain and M. Lush and F. Ducluzeau and S. Povey},
  title = {{ Genew: the Human Gene Nomenclature Database}},
  journal = {{Nucleic Acids Research}},
  year = {2002},
  volume = {30},
  pages = {{169--171}},
  number = {1}
}

@BOOK{WalChrSch97,
  title = {{ Programmieren mit Perl}},
  publisher = {{OReilly/VVA}},
  year = {1997},
  author = {Wall, L. and Christiansen, T. and Schwartz, R. L.}
}

@ARTICLE{WanMu03,
  author = {Wang, J. and Mu, Q.},
  title = {{ Soap-HT-BLAST: high throughput BLAST based on Web services}},
  journal = {{Bioinformatics}},
  year = {2002},
  volume = {19},
  pages = {1863--1864},
  number = {14}
}

@ARTICLE{WanRieRob02,
  author = {Wang, L. and Riethoven, J. J. and Robinson, A.},
  title = {{ XEMBL: distributing EMBL data in XML format}},
  journal = {{Bioinformatics}},
  year = {2002},
  volume = {18},
  pages = {1147--1148},
  number = {8}
}

@ARTICLE{WanRodRed00,
  author = {Wang, Lichun and Rodriguez-Tome, Patricia and Redaschi, Nicole and
	McNeil, Phil and Robinson, Alan and Lijnzaad, Philip},
  title = {Accessing and distributing EMBL data using CORBA (common object request
	broker architecture)},
  journal = {Genome Biology},
  year = {2000},
  volume = {1},
  pages = {research0010.1-research0010.10},
  number = {5},
  doi = {10.1186/gb-2000-1-5-research0010},
  issn = {1465-6906},
  pubmedid = {11178259},
  url = {http://genomebiology.com/2000/1/5/research/0010}
}

@ARTICLE{WarJaiNi02,
  author = {Ware, D. H. and Jaiswal, P. and Ni, J. and Yap, I. V. and Pan, X.
	
	 and Clark, K. Y. and Teytelman, L. and Schmidt, S. C. and Zhao, W.
	
	 and Chang, K. and Cartinhour, S. and Stein, L. D.
	
	
	 and McCouch, S. R.},
  title = {{ Gramene, a Tool for Grass Genomics}},
  journal = {{Plant Physiology}},
  year = {2002},
  volume = {130},
  pages = {{1606--1613}},
  number = {4}
}

@ARTICLE{WarJaiNi02b,
  author = {Ware, D. and Jaiswal, P. and Ni, J. and Pan, X. and Chang, K. and
	Clark, K. and Teytelman, L. and Schmidt, S. and Zhao, W. and Cartinhour,
	S. and McCouch, S. and Stein, L.},
  title = {{Gramene: a resource for comparative grass genomics}},
  journal = {Nucl. Acids Res.},
  year = {2002},
  volume = {30},
  pages = {103-105},
  number = {1},
  abstract = {Gramene (http://www.gramene.org) is a comparative genome mapping database
	for grasses and a community resource for rice. Rice, in addition
	to being an economically important crop, is also a model monocot
	for understanding other agronomically important grass genomes. Gramene
	replaces the existing AceDB database RiceGenes' with a relational
	database based on Oracle. Gramene provides curated and integrative
	information about maps, sequence, genes, genetic markers, mutants,
	QTLs, controlled vocabularies and publications. Its aims are to use
	the rice genetic, physical and sequence maps as fundamental organizing
	units, to provide a common denominator for moving from one crop grass
	to another and is to serve as a portal for interconnecting with other
	web-based crop grass resources. This paper describes the initial
	steps we have taken towards realizing these goals.},
  eprint = {http://nar.oxfordjournals.org/cgi/reprint/30/1/103.pdf},
  url = {http://nar.oxfordjournals.org/cgi/content/abstract/30/1/103}
}

@INPROCEEDINGS{Was90,
  author = {Wassermann, A.},
  title = {{Tool Integration in Software Engineering Environments}},
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	on Environments},
  year = {1990},
  editor = {Long, F.},
  pages = {137--149},
  publisher = { LNCS 467, Springer Verlag, Berlin}
}

@ARTICLE{WasGarKoh83,
  author = {Waser, M. and Garfinkel, L. and Kohn, C. and Garfinkel, D.},
  title = {{ Computer Modeling of Muscle Phosphofructokinase}},
  journal = {{Journal of Theoretical Biology}},
  year = {1983},
  volume = {103},
  pages = {{295--312}},
  optnumber = {000},
  publisher = {{London: Academic Press Limited}}
}

@BOOK{Wat95,
  title = {{ Introduction to Computational Biology}},
  publisher = {{London: Chapman \& Hall}},
  year = {1995},
  author = {Waterman, M.}
}

@ARTICLE{WatCri53,
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  title = {{ Genetical Implications of the Structure of Deoxyribonucleid Acid}},
  journal = {{Nature}},
  year = {1953},
  volume = {171},
  pages = {964--967},
  number = {4361}
}

@TECHREPORT{Wau00,
  author = {Waugh, M.},
  title = {PathDB helps researchers analyze metabolism},
  institution = {National Center for Genome Resources},
  year = {2000},
  number = {1},
  note = {http://www.ncgr.org/software/pathdb/},
  volume = {5}
}

@ARTICLE{WebHarWes04,
  author = {Weber, M. and Harada, E. and Vess, C. and Roepenack-Lahaye, {E. v.}
	
	 and Clemens, S.},
  title = { Comparative microarray analysis of {\em Arabidopsis thaliana} and
	
	
	 {\em Arabidopsis halleri} roots identifies nicotianamine synthase,
	
	
	 a ZIP transporter and other genes as potential metal hyperaccumulation
	factors},
  journal = {Plant Journal},
  year = {2004},
  volume = {37},
  pages = {269--281},
  number = {2},
  eprint = {http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-313X.2003.01960.x/pdf},
  url = {http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-313X.2003.01960.x/abs}
}

@INPROCEEDINGS{WeiKnuVor06,
  author = {Weise, S. and Kn{\"u}pffer, H. and Vorwald, J. and Scholz, U. and
	Grosse, I.},
  title = {Integration von ph{\"a}notypischen Daten in das Plant Data Warehouse},
  booktitle = {Ausgew{\"a}hlte Vortr{\"a}ge aus GPZ-Arbeitsgemeinschaften},
  year = {2006},
  volume = {70},
  series = {Vortr{\"a}ge f{\"u}r Pflanzenz{\"u}chtung},
  pages = {84--86},
  address = {G{\"o}ttingen},
  month = {M{\"a}rz},
  publisher = {Gesellschaft f{\"u}r Pflanzenz{\"u}chtung e.\,V.\ (GPZ)},
  language = {german}
}

@ARTICLE{WesFenJai02,
  author = {J. Westbrook and Z. Feng and S. Jain and T. N. Bhat and N. Thanki
	and V. Ravichandran and G. L. Gilliland and W. Bluhm and H. Weissig
	and D. S. Greer and P. E. Bourne and H. M. Berman},
  title = {{ The Protein Data Bank: unifying the archive}},
  journal = {{Nucleic Acids Research}},
  year = {2002},
  volume = {30},
  pages = {{245--248}},
  number = {1}
}

@ARTICLE{WheBarBen06,
  author = {Wheeler, D. L. and Barrett, T. and Benson, D. A. and Bryant, S. H.
	and Canese, K. and Chetvernin, V. and Church, D. M. and DiCuccio,
	M. and Edgar, R. and Federhen, S. and Geer, L. Y. and Helmberg, W.
	and Kapustin, Y. and Kenton, D. L. and Khovayko, O. and Lipman, D.
	J. and Madden, T. L. and Maglott, D. R. and Ostell, J. and Pruitt,
	K. D. and Schuler, G. D. and Schriml, L. M. and Sequeira, E. and
	Sherry, S. T. and Sirotkin, K. and Souvorov, A. and Starchenko, G.
	and Suzek, T. O. and Tatusov, R. and Tatusova, T. A. and Wagner,
	L. and Yaschenko, E.},
  title = {Database resources of the National Center for Biotechnology Information},
  journal = {Nucl. Acids Res.},
  year = {2006},
  volume = {34},
  pages = {D173-180},
  number = {Database issue},
  eprint = {http://nar.oxfordjournals.org/cgi/reprint/34/suppl_1/D173.pdf}
}

@ARTICLE{WheChaLas00,
  author = {Wheeler, D. L. and Chappey, C. and Lash, A. E. and Leipe, D. D. and
	Madden, T. L. and Schuler, G. D. and Tatusova, T. A. and Rapp, B.
	A.},
  title = {{ Database resources of the National Center for Biotechnology Information}},
  journal = {{Nucleic Acids Research}},
  year = {2000},
  volume = {28},
  pages = {10--14},
  number = {1}
}

@ARTICLE{WheChuFed03,
  author = {Wheeler, D. L. and Church, D. M. and Federhen, S. and Lash, A. E.
	and Madden, T. L. and Pontius, J. U. and Schuler, G. D. and Schriml,
	L. M. and Sequeira, E. and Tatusova, T. A. and Wagner, L.},
  title = {{ Database resources of the National Center for Biotechnology}},
  journal = {{ Nucleic Acids Research}},
  year = {2003},
  volume = {31},
  pages = {28-33},
  number = {1}
}

@ARTICLE{WheParCau06,
  author = {Whetzel, P.L. and Parkinson, H. and Causton, H.C. and Fan, L. and
	Fostel, J. and Fragoso, G. and Game, L. and Heiskanen, M. and Morrison,
	N. and Rocca-Serra, P. and others},
  title = {{The MGED Ontology: a resource for semantics-based description of
	microarray experiments}},
  journal = {Bioinformatics},
  year = {2006},
  volume = {22},
  pages = {866},
  number = {7}
}

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  author = {G. Wiederhold},
  title = {{Mediators in the Architecture of Future Information Systems}},
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  pages = {38--49},
  number = {3},
  month = mar
}

@ARTICLE{Wilkinson2005,
  author = {Mark Wilkinson and Heiko Schoof and Rebecca Ernst and Dirk Haase},
  title = {Bio{MOBY} successfully integrates distributed heterogeneous bioinformatics
	{W}eb {S}ervices. {T}he {P}la{N}et exemplar case.},
  journal = {Plant Physiol},
  year = {2005},
  volume = {138},
  pages = {5--17},
  number = {1},
  month = {May},
  abstract = {The burden of non-interoperability between on-line genomic resources
	is increasingly the rate-limiting step in large-scale genomic analysis.
	BioMOBY is a biological Web Service interoperability initiative that
	began as a retreat of representatives from the model organism database
	community in September, 2001. Its long-term goal is to provide a
	simple, extensible platform through which the myriad of on-line biological
	databases and analytical tools can offer their information and analytical
	services in a fully automated and interoperable way. Of the two branches
	of the larger BioMOBY project, the Web Services branch (MOBY-S) has
	now been deployed over several dozen data sources worldwide, revealing
	some significant observations about the nature of the integrative
	biology problem; in particular, that Web Service interoperability
	in the domain of bioinformatics is, unexpectedly, largely a syntactic
	rather than a semantic problem. That is to say, interoperability
	between bioinformatics Web Services can be largely achieved simply
	by specifying the data structures being passed between the services
	(syntax) even without rich specification of what those data structures
	mean (semantics). Thus, one barrier of the integrative problem has
	been overcome with a surprisingly simple solution. Here, we present
	a non-technical overview of the critical components that give rise
	to the interoperable behaviors seen in MOBY-S and discuss an exemplar
	case, the PlaNet consortium, where MOBY-S has been deployed to integrate
	the on-line plant genome databases and analytical services provided
	by a European consortium of databases and data service providers.},
  doi = {10.1104/pp.104.059170},
  keywords = {, , 15888673},
  pii = {138/1/5},
  pmid = {15888673},
  url = {http://dx.doi.org/10.1104/pp.104.059170}
}

@ARTICLE{WilLin02,
  author = {Wilkinson, M. D. and Links, M.},
  title = {{ BioMOBY: An open source biological web services proposal}},
  journal = {{Briefings in Bioinformatics}},
  year = {2002},
  volume = {3},
  pages = {331--341},
  number = {4},
  file = {wilkinson_links_2002.pdf:Systeme\\BioMOBY\\wilkinson_links_2002.pdf:PDF}
}

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	I. and Schacherer, F.},
  title = {{ TRANSFAC: an integrated system for gene expression regulation}},
  journal = {{Nucleic Acids Research}},
  year = {2000},
  volume = {28},
  pages = {316--319},
  number = {1}
}

@ARTICLE{WinDieKar96,
  author = {Wingender, E. and Dietze, P. and Karas, H. and Kn{\"u}ppel, R.},
  title = {{ TRANSFAC: A database on transcription factors and their DNA binding
	sites}},
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  volume = {24},
  pages = {238--241},
  number = {1}
}

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  author = {Wingender, E. and Karas, H. and Kn{\"u}ppel, R.},
  title = {{ TRANSFAC~--~Database as a Bridge between Sequence Data Libraries
	and Biological Function}},
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  year = {1997},
  editor = {Altman, R. B. and Dunker, A. K. and Hunter, L. and Klein, T. E.},
  pages = {477--485},
  publisher = {Singapore et al.: World Scientific}
}

@INPROCEEDINGS{Won00,
  author = {Wong, L.},
  title = {{Kleisli, its Exchange Format, Supporting Tools, and an application
	in Protein Interaction Extraction}},
  booktitle = {{BIBE 2000: IEEE International Symposium on Bio-Informatic \& Biomedical
	Engineering, Washington, D.C., U.S.A., November 8-10}},
  year = {2000},
  pages = {21--28},
  publisher = {{IEEE Computer Society}}
}

@INPROCEEDINGS{WonLamGra00,
  author = {Wong, R. K. and Lam, F. and Graham, S. and Shui, W.},
  title = {{An XML Repository for Molecular Sequence Data}},
  booktitle = {{BIBE 2000: IEEE International Symposium on Bio-Informatic \& Biomedical
	Engineering, Washington, D.C., U.S.A., November 8-10}},
  year = {2000},
  pages = {35--42},
  publisher = {{IEEE Computer Society}}
}

@UNPUBLISHED{wordnet,
  author = {{Cognitive Science Laboratory at Princeton University}},
  title = {{WordNet -- a lexical database for the english language}},
  note = {http://www.cogsci.princeton.edu/~wn/},
  key = {wordnet}
}

@ARTICLE{WroSteGob03,
  author = {Wroe,C. and Stevens,R. and Goble,C. and Roberts,A. and Greenwood,M.},
  title = {{A suite of DAML+OIL ontologies to describe bioinformatics web services
	and data}},
  journal = {{Intl J. Coop. Inform. Systems}},
  year = {2003},
  volume = {12}
}

@ARTICLE{WuApwBai06,
  author = {Wu, C.H. and Apweiler, R. and Bairoch, A. and Natale, D.A. and Barker,
	W.C. and Boeckmann, B. and Ferro, S. and Gasteiger, E. and Huang,
	H. and Lopez, R. and others},
  title = {{The Universal Protein Resource (UniProt): an expanding universe
	of protein information}},
  journal = {Nucleic Acids Research},
  year = {2006},
  volume = {34},
  pages = {D10--D15},
  publisher = {Oxford Univ Press}
}

@ARTICLE{WuHuaArm02,
  author = {Wu, C. H. and Huang, H. and Arminski, L. and Castro-Alvear, J. and
	Chen, Y. and Hu, Z. and Ledley, R. S. and Lewis, K. C. and Mewes,
	H.-W. and Orcutt, B. C. and Suzek, B. E. and Tsugita, A. and Vinayaka,
	C. R. and Leh, L. L. and Zhang, J. and Barker, W. C.},
  title = {{ The Protein Information Resource: an integrated public resource
	of functional annotation of proteins}},
  journal = {{Nucleic Acids Research}},
  year = {2002},
  volume = {30},
  pages = {{35--37}},
  number = {1}
}

@ARTICLE{XenSalDua02,
  author = {I. Xenarios and L. Salw�ski and X. J. Duan and P. Higney and S.
	Kim and D. Eisenberg},
  title = {{ DIP, the Database of Interacting Proteins: a research tool for
	studying cellular networks of protein interactions}},
  journal = {{Nucleic Acids Research}},
  year = {2002},
  volume = {30},
  pages = {{303--305}},
  number = {1}
}

@ARTICLE{XieDemBle00,
  author = {Xie, G. and DeMarco, R. and Blevis, R. and Wang, Y.},
  title = {{ Storing biological sequence databases in relational form}},
  journal = {{Bioinformatics}},
  year = {2000},
  volume = {16},
  pages = {288--289},
  number = {3}
}

@ARTICLE{XieHoo03,
  author = {Xie, T. and Hood, L.},
  title = {{ ACGT-a comparative genomics tool}},
  journal = {{Bioinformatics}},
  year = {2003},
  volume = {19},
  pages = {1039--1040},
  number = {8}
}

@MISC{xml,
  author = {{World Wide Web Consortium} {XML-W3C}},
  title = {Extensible Markup Language (XML)},
  url = {www.w3.org/XML/}
}

@INPROCEEDINGS{xml-ql,
  author = {Deutsch, A. and Fernandez, M. and Florescu, D. and Levy, A. and Suciu,
	D.},
  title = {{A Query Language for XML}},
  note = {http://www8.org/w8-papers/1c-xml/query/query.html},
  key = {xml-ql}
}

@UNPUBLISHED{xmlschema,
  author = {{World Wide Web Consortium (W3C)}},
  title = {{XML Schema}},
  note = {http://www.w3.org/XML/Schema},
  key = {xmlschema}
}

@INPROCEEDINGS{xql,
  author = {{World Wide Web Consortium (W3C)}},
  title = {{XML Query Language (XQL)}},
  editor = {Robie, J. and Lapp, J. and Schach, D.},
  note = {http://www.w3.org/TandS/QL/QL98/pp/xql.html},
  key = {xql}
}

@MISC{Xquery-old,
  author = {W3C},
  title = {{XML} {Q}uery},
  year = {2003},
  note = {\http://www.w3.org/XML/Query}
}

@MISC{xquery01,
  author = {World Wide Web Consortium {W3C}},
  title = {{XQuery:} The {W3C} query language for {XML} -- {W3C} working draft},
  howpublished = {Available at http://www.w3.org/TR/xquery/},
  year = {2001},
  url = {http://www.w3.org/TR/xquery/}
}

@ARTICLE{YeMcgMad06,
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  title = {{BLAST: improvements for better sequence analysis}},
  journal = {Nucl. Acids Res.},
  year = {2006},
  volume = {34},
  pages = {W6-9},
  number = {suppl\_2},
  doi = {10.1093/nar/gkl164},
  eprint = {http://nar.oxfordjournals.org/cgi/reprint/34/suppl_2/W6.pdf},
  url = {http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_2/W6}
}

@ARTICLE{YonLinLin00,
  author = {Yona, G. and Linial, N. and Linial, M.},
  title = {{ ProtoMap: automatic classification of protein sequences and hierarchy
	of protein families}},
  journal = {{Nucleic Acids Research}},
  year = {2000},
  volume = {28},
  pages = {49--55},
  number = {1}
}

@INPROCEEDINGS{ZdoLopApw00,
  author = {Zdobnov, E. M. and Lopez, R.and Apweiler, R. and Etzold, T.},
  title = {{ The EBI SRS server - recent developments}},
  booktitle = {{ Proceedings of the German Conference on Bioinformatics (GCB '00),
	Heidelberg, October 5-7}},
  year = {2000},
  editor = {Bornberg-Bauer, E. and Rost, U. and Stoye, J. and Vingron, M.},
  pages = {139--147},
  isbn = {{3-89722-498-4}},
  optpublisher = {XXX}
}

@ARTICLE{ZdoLopApw02,
  author = {Zdobnov, E. M. and Lopez, R. and Apweiler, R.
	
	 and Etzold, T.},
  title = {{ The EBI SRS server -- new features}},
  journal = {{Bioinformatics}},
  year = {2002},
  volume = {18},
  pages = {1149--1150},
  number = {8}
}

@ARTICLE{ZhaJin03,
  author = {Zhang, K. and Jin, L.},
  title = {{ HaploBlockFinder: haplotype block analyses}},
  journal = {{Bioinformatics}},
  year = {2003},
  volume = {19},
  pages = {1300--1301},
  number = {10}
}

@ARTICLE{ZhoLiWon03,
  author = {Zhong, S. and Li, C. and Wong, W. H.},
  title = {{ ChipInfo: software for extracting gene annotation and gene 
	
	 ontology information for microarray analysis}},
  journal = {{Nucleic Acids Research}},
  year = {2003},
  volume = {31},
  pages = {{3483--3486}},
  number = {13}
}

@ARTICLE{ZhuSchBre03,
  author = {Zhu, W. and Schlueter, S. D. and Brendel, V.},
  title = {{ Refined Annotation of the Arabidopsis Genome by 
	
	 Complete Expressed Sequence Tag Mapping}},
  journal = {{Plant Physiology}},
  year = {2003},
  volume = {132},
  pages = {{469--484}},
  number = {2}
}

@ARTICLE{ZimHenGru05,
  author = {Zimmermann, P. and Hennig, L. and Gruissem, W.},
  title = {{Gene-expression analysis and network discovery using Genevestigator.}},
  journal = {Trends Plant Sci},
  year = {2005},
  volume = {10},
  pages = {407--9},
  number = {9}
}
@inproceedings{HipKorToe10,
  author    = {Klaus Hippe and
               Benjamin Kormeier and
               Thoralf T{\"o}pel and
               Sebastian Janowski and
               Ralf Hofest{\"a}dt},
  title     = {{DAWIS-M.D.} - A Data Warehouse System for Metabolic Data},
  booktitle = {GI Jahrestagung (2)},
  year      = {2010},
  pages     = {720-725},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
